#include <sequence_map_aligned.hpp>

Collaboration diagram for vdj_pipe::Seq_map_aligned:

[legend]

Classes
struct	Err

struct	Match

Public Types
typedef Id_iterator< Seq_id >	iterator

typedef iterator	const_iterator

Public Member Functions
	Seq_map_aligned ()

iterator	begin () const

iterator	end () const

Seq_id	max_id () const

std::size_t	size () const

void	load_file (std::string const &fasta, const bool reverse)

void	insert (std::string const &id, std::string seq, const bool reverse)

Seq_entry const &	seq (const Seq_id sid) const

std::string const &	seq_id (const Seq_id sid) const

Match	best_match (const boost::string_ref seq, const std::size_t min_match, const bool track_mismatches) const

detail::Vector_set< Seq_id >	find_overlaping (const boost::string_ref seq, const std::size_t min_match) const

Private Types
typedef gdst::Gdst	suffix_tree

typedef suffix_tree::seq_map	seq_map

typedef detail::Id_bimap< Seq_id, std::string >	id_map

Static Private Member Functions
static void	check (const boost::string_ref seq)

Private Attributes
suffix_tree	st_

id_map	idm_

Member Typedef Documentation

typedef iterator vdj_pipe::Seq_map_aligned::const_iterator

typedef detail::Id_bimap<Seq_id, std::string> vdj_pipe::Seq_map_aligned::id_map

private

typedef Id_iterator<Seq_id> vdj_pipe::Seq_map_aligned::iterator

typedef suffix_tree::seq_map vdj_pipe::Seq_map_aligned::seq_map

private

typedef gdst::Gdst vdj_pipe::Seq_map_aligned::suffix_tree

private

Constructor & Destructor Documentation

vdj_pipe::Seq_map_aligned::Seq_map_aligned ( )

inline

Member Function Documentation

iterator vdj_pipe::Seq_map_aligned::begin ( ) const

inline

Match vdj_pipe::Seq_map_aligned::best_match	(	const boost::string_ref	seq,
		const std::size_t	min_match,
		const bool	track_mismatches
	)		const

inline

static void vdj_pipe::Seq_map_aligned::check ( const boost::string_ref seq )

inlinestaticprivate

iterator vdj_pipe::Seq_map_aligned::end ( ) const

inline

detail::Vector_set<Seq_id> vdj_pipe::Seq_map_aligned::find_overlaping	(	const boost::string_ref	seq,
		const std::size_t	min_match
	)		const

inline

void vdj_pipe::Seq_map_aligned::insert	(	std::string const &	id,
		std::string	seq,
		const bool	reverse
	)

inline

void vdj_pipe::Seq_map_aligned::load_file	(	std::string const &	fasta,
		const bool	reverse
	)

inline

Seq_id vdj_pipe::Seq_map_aligned::max_id ( ) const

inline

Seq_entry const& vdj_pipe::Seq_map_aligned::seq ( const Seq_id sid ) const

inline

std::string const& vdj_pipe::Seq_map_aligned::seq_id ( const Seq_id sid ) const

inline

std::size_t vdj_pipe::Seq_map_aligned::size ( ) const

inline

Member Data Documentation

id_map vdj_pipe::Seq_map_aligned::idm_

private

suffix_tree vdj_pipe::Seq_map_aligned::st_

private

The documentation for this class was generated from the following file:

lib/sequence_map_aligned.hpp

Classes

Public Types

Public Member Functions

Private Types

Static Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation